Halophiles: Genetics and Genomes

210 Pages·2014·9.15 MB·English

by  R Thane Papke

Halophiles
Genetics and Genomes
Edited by
R. Thane Papke
and
Aharon Oren
Caister Academic Press
Halophiles
Genetics and Genomes
Edited by
R. Thane Papke
Department of Molecular and Cell Biology
University of Connecticut
Storrs, CT
USA
and
Aharon Oren
Department of Plant and Environmental Sciences
The Hebrew University of Jerusalem
Jerusalem
Israel
Caister Academic Press
Copyright © 2014
Caister Academic Press
Norfolk, UK
www.caister.com
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library
ISBN: 978-1-908230-42-3 (hardback)
ISBN: 978-1-908230-65-2 (ebook)
Description or mention of instrumentation, software, or other products in
this book does not imply endorsement by the author or publisher. The author
and publisher do not assume responsibility for the validity of any products or
procedures mentioned or described in this book or for the consequences of
their use.
All rights reserved. No part of this publication may be reproduced, stored in
a retrieval system, or transmitted, in any form or by any means, electronic,
mechanical, photocopying, recording or otherwise, without the prior
permission of the publisher. No claim to original U.S. Government works.
Cover design adapted from photos taken by Scott Chimileski, Department of
Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
Contents
Contributors v
Preface ix
1 Ecology and Evolution of Haloquadratum walsbyi
Through the Lens of Genomics and Metagenomics 1
Lejla Pašić and Francisco Rodríguez-Valera
2 Salinibacter ruber: The Never Ending Microdiversity? 37
Arantxa Peña, María Gomariz, Marianna Lucio, Pedro González-
Torres, Jaime Huertas-Cepa, Manuel Martínez-García, Fernando
Santos, Phillippe Schmitt-Kopplin, Toni Gabaldón, Ramon
Rosselló-Móra and Josefa Antón
3 Horizontal Gene Transfer in Halobacteria 57
Matthew S. Fullmer, J. Peter Gogarten and R. Thane Papke
4 Comparative Genomics of Haloarchaeal Viruses 77
Elina Roine
5 Microbial Adaptation to Saline Environments: Lessons
from the Genomes of Natranaerobius thermophilus and
Halobacillus halophilus 107
Noha M. Mesbah, Inga Hänelt, Baisuo Zhao and Volker Müller
6 Staying in Shape: The Haloarchaeal Cell Wall 129
Jerry Eichler, Adi Arbiv, Chen Cohen-Rosenzweig, Lina Kaminski,
Lina Kandiba, Zvia Konrad and Shai Naparstek
7 Cell Cycle and Polyploidy in Haloarchaea 145
Karolin Zerulla, Anke Baumann and Jörg Soppa
iv | Contents
8 Cell Regulation by Proteolytic Systems and Protein Conjugation 167
Julie Maupin-Furlow
Index 195
Contributors
Josefa Antón Jerry Eichler
Department of Physiology, Genetics and Department of Life Sciences
Microbiology Ben Gurion University
University of Alicante Beersheva
Alicante Israel
Spain
[email protected]
[email protected]
Matthew S. Fullmer
Adi Arbiv Department of Molecular and Cell Biology
Department of Life Sciences University of Connecticut
Ben Gurion University Storrs, CT
Beersheva USA
Israel
[email protected]
[email protected]
Toni Gabaldón
Anke Baumann Pompeu Fabra University (UPF); and
Institute for Molecular Biosciences Bioinformatics and Genomics Programme
Goethe University Frankfurt am Main Centre for Genomic Regulation (CRG)
Frankfurt am Main Barcelona
Germany Spain
[email protected] [email protected]
Chen Cohen-Rosenzweig J. Peter Gogarten
Department of Life Sciences Department of Molecular and Cell Biology
Ben Gurion University University of Connecticut
Beersheva Storrs, CT
Israel USA
[email protected] [email protected]
vi | Contributors
María Gomariz Lina Kandiba
Evolutionary Genomics Group Department of Life Sciences
Department of Physiology, Genetics and Ben Gurion University
Microbiology; and Beersheva
Department of Materials Israel
Optics and Electronics
[email protected]
University Miguel Hernández
Elche
Zvia Konrad
Alicante
Department of Life Sciences
Spain
Ben Gurion University
[email protected] Beersheva
Israel
Pedro González-Torres
[email protected]
Department of Physiology, Genetics and
Microbiology
Marianna Lucio
University of Alicante
Research Unit Analytical BioGeoChemistry
Alicante
Helmholtz Zentrum Munich, German
Spain
Research Center for Environmental Health
[email protected] Neuherberg
Germany
Inga Hänelt
[email protected]
Department of Molecular Microbiology and
Bioenergetics
Manuel Martínez-García
Goethe University Frankfurt am Main
Department of Physiology, Genetics and
Frankfurt am Main
Microbiology
Germany
University of Alicante
[email protected] Alicante
Spain
Jaime Huertas-Cepa
[email protected]
Pompeu Fabra University (UPF); and
Bioinformatics and Genomics Programme
Julie Maupin-Furlow
Centre for Genomic Regulation (CRG)
Department of Microbiology and Cell Science
Barcelona
University of Florida
Spain
Gainesville, FL
[email protected] USA
[email protected]
Lina Kaminski
Department of Life Sciences
Noha M. Mesbah
Ben Gurion University
Department of Biochemistry
Beersheva
Faculty of Pharmacy
Israel
Suez Canal University
[email protected] Ismailia
Egypt
[email protected]
Contributors | vii
Volker Müller Arantxa Peña
Department of Molecular Microbiology and Department of Physiology, Genetics and
Bioenergetics Microbiology
Goethe University Frankfurt am Main University of Alicante
Frankfurt am Main Alicante; and
Germany Department of Biology-Microbiology
University of Balearic Islands
[email protected]
Palma de Mallorca
Balearic Islands
Shai Naparstek
Spain
Department of Life Sciences
Ben Gurion University [email protected]
Beersheva
Israel Francisco Rodríguez-Valera
Evolutionary Genomics Group
[email protected]
División de Microbiología
Universidad Miguel Hernández
Aharon Oren
San Juan de Alicante
Department of Plant and Environmental
Spain
Sciences
The Institute of Life Sciences [email protected]
The Hebrew University of Jerusalem
Jerusalem Elina Roine
Israel Department of Biosciences
University of Helsinki
[email protected]
Helsinki
Finland
R. Thane Papke
Department of Molecular and Cell Biology [email protected]
University of Connecticut
Storrs, CT Ramon Rosselló-Móra
USA Marine Microbiology Group
Department of Ecology and Marine Resources
[email protected]
Institut Mediterrani d’Estudis Avançast
IMEDEA (CSIC-UIB)
Lejla Pašić
Esporles
Department of Biology
Balearic Islands
Biotechnical Faculty
Spain
University of Ljubljana
Ljubljana [email protected]
Slovenia
Fernando Santos
[email protected]
Department of Physiology, Genetics and
Microbiology
University of Alicante
Alicante
Spain
[email protected]
viii | Contributors
Phillippe Schmitt-Kopplin Karolin Zerulla
Research Unit Analytical BioGeoChemistry Institute for Molecular Biosciences
Helmholtz Zentrum Munich, German Goethe University Frankfurt am Main
Research Center for Environmental Health Frankfurt am Main
Neuherberg; and Germany
Analytical Food Chemistry Department
[email protected]
Technische Universität München
Freising-Weihenstephan
Baisuo Zhao
Germany
Graduate School Chinese
[email protected]\ Academy of Agricultural Sciences
Beijing
Jörg Soppa China
Institute for Molecular Biosciences
[email protected]
Goethe University Frankfurt am Main
Frankfurt am Main
Germany
[email protected]
Preface
Admittedly, it is trying to study microorganisms whose growth media fills the labora-
tory with steam, or the centrifuge heads with salt, or which grow so slowly that weeks,
instead of hours, may be required for experiments and whose genetics are unknown or
almost impossible to study.
These words were written by the late Donn Kushner (1927–2001) in his introduction to his
book Microbial Life in Extreme Environments (Kushner, 1978a). Although much progress has
been made in the 35 years that have passed since, the message is still perfectly true. Some of
the most intriguing halophiles such as the flat square archaeon Haloquadratum walsbyi are
still very difficult to grow and at best grow very slowly. Genetic systems have been developed
only for a limited number of extremely halophilic Archaea, and a few moderately halophilic
Bacteria. But thanks to the development of genetic systems for organisms such as Halobacte-
rium salinarum, Haloferax volcanii (Euryarchaeota) and Halobacillus halophilus (Firmicutes)
we now have a fair number of model organisms in which the molecular biology of diverse
groups of halophilic microorganisms can be studied. Modern molecular techniques of
genomics and culture-independent methods of metagenomics have also contributed much
towards our understanding of the functioning of a wide range of halophilic microorganisms
and their viruses.
This book contains eight essays covering different aspects of the genetics and the genom-
ics of halophiles, with special emphasis on those topics in which significant progress has
been made in recent years. Organisms featured are extreme as well as moderate halophiles,
types that grow at neutral as well as alkaline pH, species that prefer moderate as well as high
temperatures for growth.
The first chapters mainly deal with genomic and culture-independent metagenomic
approaches to understanding the diversity and evolution of halophiles in their natural
environment. Cultures of Haloquadratum walsbyi are now available, but they are difficult
to handle. However, very much has been learned about their properties by culture-inde-
pendent approaches, as shown in Chapter 1 by Lejla Pašić and Francisco Rodríguez-Valera.
Salinibacter ruber is an extremely halophilic member of the Bacteria resembling in many
properties the halophilic Archaea. It was discovered little over a decade ago, and also here
genomic and metagenomic approaches have greatly increased our understanding of its
biology (Chapter 2 by Aranxa Peña and co-workers). In Chapter 3, Matthew Fullmer and
his colleagues document the frequency and wide-spread nature of horizontal gene transfer
(HGT) among the haloarchaea in their natural environment, and provide conjecture on